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comparison macros.xml @ 48:2f457890d8c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
author iuc
date Tue, 11 Dec 2018 13:59:34 -0500
parents 71d71721695e
children df28283b3778
comparison
equal deleted inserted replaced
47:33c2e424ad7d 48:2f457890d8c8
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.27.0">bedtools</requirement> 4 <requirement type="package" version="@WRAPPER_VERSION@">bedtools</requirement>
5 <yield/> 5 <yield/>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8 <token name="@WRAPPER_VERSION@">2.27.0</token> 8 <token name="@WRAPPER_VERSION@">2.27.1</token>
9 <token name="@SAMTOOLS_VERSION@">1.2</token> 9 <token name="@SAMTOOLS_VERSION@">1.9</token>
10 <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf</token> 10 <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf</token>
11 <token name="@STD_BEDTOOLS_INPUT_LABEL@">bed,bedgraph,gff,vcf</token> 11 <token name="@STD_BEDTOOLS_INPUT_LABEL@">bed,bedgraph,gff,vcf</token>
12 <xml name="stdio"> 12 <xml name="stdio">
13 <stdio> 13 <stdio>
14 <!-- Anything other than zero is an error --> 14 <!-- Anything other than zero is an error -->
19 <regex match="Exception:" /> 19 <regex match="Exception:" />
20 </stdio> 20 </stdio>
21 <version_command>bedtools --version</version_command> 21 <version_command>bedtools --version</version_command>
22 </xml> 22 </xml>
23 <xml name="reciprocal"> 23 <xml name="reciprocal">
24 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" 24 <param name="reciprocal" argument="-r" type="select" label="Require that the fraction of overlap be reciprocal for A and B" help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.">
25 label="Require that the fraction of overlap be reciprocal for A and B" 25 <option value="" selected="True">No</option>
26 help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B. (-r)" /> 26 <option value="-r">Yes</option>
27 </param>
27 </xml> 28 </xml>
28 <xml name="overlap"> 29 <xml name="overlap">
29 <param name="overlap" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" help="Default is 1E-9, i.e. 1bp. (-f)"/> 30 <param name="overlap" argument="-f" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" help="Default is 1E-9, i.e. 1bp."/>
31 </xml>
32 <xml name="overlapB">
33 <param name="overlapB" argument="-F" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" help="Default is 1E-9, i.e. 1bp."/>
30 </xml> 34 </xml>
31 <xml name="strand2"> 35 <xml name="strand2">
32 <param name="strand" type="select" label="Calculation based on strandedness?"> 36 <param name="strand" type="select" label="Calculation based on strandedness?">
33 <option value="" selected="True">Overlaps on either strand</option> 37 <option value="" selected="True">Overlaps on either strand</option>
34 <option value="-s">Only overlaps occurring on the **same** strand.</option> 38 <option value="-s">Only overlaps occurring on the **same** strand.</option>